Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Error while running GATK UnifiedGenotyper

    Hi everyone!
    I've been analyzing some illumina whole exome sequencing data these days. yesterday I used GATK(version 2.0) UnifiedGenotyper to call snps and indels with the following commands:
    run_gatk.sh
    -T UnifiedGenotyper
    -R GRCh37/human_g1k_v37.fasta
    -I GATK_recal_result.bam
    -glm BOTH
    --dbsnp reference/dbsnp_134.b37.vcf
    -stand_call_conf 50
    -stand_emit_conf 10
    -o raw2.vcf
    -dcov 200
    --num_threads 10

    After running theses commands, I got a vcf file which is very small(when I checked the vcf file, I found these called snps and indels are all from Chromosome1)
    The error message is as follows:
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR stack trace
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to merge temporary Tribble output file.
    at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.mergeExistingOutput(HierarchicalMicroScheduler.java:269)
    at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:105)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:269)
    at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
    Caused by: org.broad.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: /rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp (Too many open files), for input source: /rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp
    at org.broad.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:104)
    at org.broad.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:58)
    at org.broad.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:69)
    at org.broadinstitute.sting.gatk.io.storage.VariantContextWriterStorage.mergeInto(VariantContextWriterStorage.java:182)
    at org.broadinstitute.sting.gatk.io.storage.VariantContextWriterStorage.mergeInto(VariantContextWriterStorage.java:52)
    at org.broadinstitute.sting.gatk.executive.OutputMergeTask.merge(OutputMergeTask.java:48)
    at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.mergeExistingOutput(HierarchicalMicroScheduler.java:263)
    ... 6 more
    Caused by: java.io.FileNotFoundException: /rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp (Too many open files)
    at java.io.FileInputStream.open(Native Method)
    at java.io.FileInputStream.<init>(FileInputStream.java:120)
    at org.broad.tribble.util.ParsingUtils.openInputStream(ParsingUtils.java:56)
    at org.broad.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:96)
    ... 12 more
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version 2.0-39-gd091f72):
    ##### ERROR
    ##### ERROR Please visit the wiki to see if this is a known problem
    ##### ERROR If not, please post the error, with stack trace, to the GATK forum
    ##### ERROR Visit our website and forum for extensive documentation and answers to
    ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ##### ERROR
    ##### ERROR MESSAGE: Unable to merge temporary Tribble output file.
    ##### ERROR ------------------------------------------------------------------------------------------
    Would you please help me solve it ? Thanks a lot
    Dona

  • #2
    You'll likely have more luck getting an answer to your question by reading the GATK documentation and then posting a question at the official GATK forums (http://gatkforums.broadinstitute.org/), as stated in your error message.

    Comment


    • #3
      As already said, ask the GATK developers, they're very responsive to questions.

      Having said that I had a very similar issue with an older release:

      /rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp (Too many open files)

      Might suggest that you've hit the per-user ulimit, on our servers I had to up the ulimit for users running UG (although the bug that was creating this issue in the 1.x series was subsequently fixed).

      Comment


      • #4
        Thanks a lot!
        I sent this error message to the server programmer, after he changed some of the system configure (in /etc/security/limit.conf), I run these commands again with num_threads reducing to 2, and it worked~

        Comment


        • #5
          thanks!
          I have solved this problem with the server programmer's help
          some of the system configre(in /etc/sequrity/limit.conf)should be changed

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Strategies for Sequencing Challenging Samples
            by seqadmin


            Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
            03-22-2024, 06:39 AM
          • seqadmin
            Techniques and Challenges in Conservation Genomics
            by seqadmin



            The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

            Avian Conservation
            Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
            03-08-2024, 10:41 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Yesterday, 06:37 PM
          0 responses
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          9 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          49 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          67 views
          0 likes
          Last Post seqadmin  
          Working...
          X